The Regional Virus Laboratory is the only CPA accredited provider of virology services in N. Ireland.

Transcription

1 Regional Virus Laboratory The Regional Virus Laboratory is the only CPA accredited provider of virology services in N. Ireland. The full postal address is: Regional Virus Laboratory Kelvin Building Royal Victoria Hospital Grosvenor Road Belfast BT12 6BA Contact Details Telephone: direct line Fax: RVH Switchboard Consultant virologists Dr Peter V Coyle Phone RVH ext peter.coyle@belfasttrust.hscni.net Dr Conall McCaughey Phone RVH ext conall.mccaughey@belfasttrust.hscni.net Principal Virologist Ms Dorothy E Wyatt Phone RVH ext dorothy.wyatt@belfasttrust.hscni.net Operational Manager Molecular Services Mr Eric Mitchell Phone RVH ext frederick.mitchell@belfasttrust.hscni.net Operational Manager Serology Mr Desy Smart Phone RVH ext desy.smart@belfasttrust.hscni.net

2 General Information Normal laboratory opening hours: Monday-Thursday hours Friday hours Out of hours emergency service: Telephone the Royal Hospitals switchboard ( ) to contact the Virology Biomedical Scientist on call. The laboratory provides an on-call service principally for testing organ donors. Other out of hours emergency requests should be discussed with the Virology Biomedical Scientist on call in the first instance. If necessary, out of hours requests and requests for medical advice may be referred to a consultant virologist. General notes about the use of the RVL Nucleic acid detection using polymerase chain reaction (PCR) for viral nucleic acid (either RNA or DNA) is our front-line assay to detect many viral pathogens. Preferred specimens are generally from the body system where the virus is and should be collected as early as possible in the illness. For example, in suspected respiratory infection please collect respiratory specimens and in patients with a vesicular rash collect vesicle fluid, rather than blood for antibodies. Clotted blood samples for serology remain useful, especially for HIV, hepatitis viruses, erythrovirus B19, measles, rubella and Epstein Barr virus. We do not perform serology testing for respiratory or gastrointestinal viruses. Tests for Post-vaccine testing for is available for hepatitis B and rubella. It is NOT recommended for measles, mumps, VZV and HAV as the assays used are not sensitive enough for vaccine induced IgG. We can test for from natural exposure to CMV, EBV, erythrovirus B19, HAV, measles and VZV. Acute and convalescent samples For some acute infections, testing both acute and convalescent sera with a time gap of 10 days can be useful. Even in illnesses such as varicella, where an IgM test is available, this can be negative early in infection, so a repeat sample may be needed. Salivary IgM Antibody Public Health medicine, through the CCDC, provide a saliva collection kit for patients who may have had recent measles, mumps or rubella. Why we may ask for a second sample To confirm certain positive results (e.g. HIV antibody positives) To investigate an evolving antibody profile or seroconversion Problems with the samples in the assay performed Insufficient or incorrect samples or a problem with the quality of the sample e.g. lysed blood.

3 Urgent specimens Pregnant, in recent contact with a case of chickenpox. If there is convincing evidence of chickenpox in the past, no testing is necessary. Otherwise, please supply details of date of contact and type of contact (face-to-face / same room for 15 minutes / own child). For all other urgent testing please phone the laboratory so that we can identify your patient s specimen. Always include a contact number on the request form. Request forms Write the following information on a request form and send it with the specimen to the RVL. Patient name, sex and date of birth Clinical history including date of onset Type and date of specimen Doctor s name, address, telephone number and cypher number if applicable Please avoid the terms viral screening, routine virology, viral studies or viral titres as these terms are confusing and unhelpful. Instead, please provide brief patient clinical details and duration of illness, which allows us to choose appropriate tests. Please do not send request forms without the patient s date of birth. Dedicated forms for specific services are available from the documents section of the laboratory website: IgM tests Virus specific IgM tests may be done on a single sample of serum for the diagnosis of acute infections for the viruses indicated in Table 1. IgM is usually positive by day 5 post-onset. Collection and transport of specimens Specimens should be clearly labelled and dated. Place all specimens in leak proof containers in sealed plastic bags. Place the request form in the extra pocket of the plastic bag or attach it outside with an elastic band. Do not staple the form to the plastic bag. Specimens suspected of containing a blood borne virus e.g. HIV, HBV or HCV should be labelled with an appropriate hazard warning sticker. Users should comply with current Royal Mail Guidelines when posting samples to the laboratory. Serology: Send a 5ml sample of clotted blood. Acceptable blood tubes are: NsV code Vol Greiner code Description (CSA ref) (on side of tube) KCM317 6ml Red top 6ml tube without gel (screw top) KCM318 6ml Red top 6ml tube without gel (flip top) KCR615 5ml Red top 5ml tube with gel (screw top) KCR616 5ml Gold top 5ml tube with gel (screw top) KCR617 5ml Gold top 5ml tube with gel (flip top) Do not send short (4ml) tubes.

4 Molecular detection: Specimens should reach the RVL with minimum delay. The specimens most frequently required are listed in Table 1, although other specimens may be requested by the RVL for some investigations. Please read the notes below. Blood: Please read Table 1 - e.g. for CMV viraemia determination send blood in a standard EDTA tube and for HCV PCR send clotted blood. Chlamydia Specimens: All swab and urine specimens must be sent in Abbott multi- Collect specimen Collection Kits which are available from the laboratories where you normally obtain supplies.i.e. Belfast City, Mater, Royal Victoria and Ulster Hospitals. Do not pre-moisten the swab with transport medium, which is a skin and eye irritant. It is only necessary to send one specimen per patient for chlamydia as follows: Females: Urine OR endocervical swab OR vulvovaginal swab Males: Urine Urine Advise patients not to urinate for one hour before sample collection. Collect the first 20-30ml (not a mid-stream sample) in a suitable foil or plastic container with no preservatives. Use the transfer pipette to transfer enough urine to the transport tube so that the liquid level is in the clear fill window. Cap tightly. Swabs Remove any mucus before using the swab from the collection kit to collect cells (vaginal, endocervical or urethral). Place the swab, tip down, in the transport tube and break it carefully at the scored line. Cap tightly. Conjunctival swabs Chlamydial conjunctivitis usually has a later onset than gonococcal conjunctivitis; the incubation period is 5-14 days. Wipe away any muco-purulent material and swab the affected eye(s) with the swab from the collection kit. Place the swab, tip down, in the transport tube and break it carefully at the scored line. Cap tightly. Place the specimen in a plastic bag and seal. Attach a completed request form [Chlamydia (non GUM clinic) May 06], available to download from the Virology Request Forms section of the laboratory website, to the specimen e.g. with an elastic band (do not staple). After collection and addition to the transport tube, the specimens are stable at ambient temperature (2 C 30 C) for up to 14 days. CSF and other fluids such as pleural or pericardial fluid : Send in a sterile bottle. Ideally send at least 1ml of CSF. Faeces & vomit: Collect specimen in a sterile container. Do not add fixatives or transport medium. Post-mortem or biopsy specimens: Place each organ specimen in a separate sterile labelled container. Do not add formalin or other fixatives. Take specimens from the main system affected, as well as faeces and a blood clot. Tissue specimens collected at postmortem should be taken aseptically and in a planned order to avoid contamination from the gastrointestinal tract. Separate sterile instruments should be used for each organ. Where

5 spongiform encephalopathy is part of the differential diagnosis this should be made clear on the request form. Respiratory specimens: Nasopharyngeal secretions: Aspirate secretions into a sterile plastic mucus extractor; transport the mucus extractor with the secretions to the RVL. Nasal wash, sputum, tracheal secretions, bronchoalveolar lavage (BAL ) : send in a sterile container. Throat and nasal swabs: break the swab into UTM or enat medium* Skin and vesicular lesions: gently scrape the base of the vesicle with a disposable scalpel blade, wipe the small amount of fluid and material adhering to the blade on the centre of a clean glass slide and air dry. Alternatively, aspirate large vesicles and send the fluid in a sterile container. For suspected orf infection: scrape the granulation tissue underlying the skin with a disposable scalpel blade, transfer the material to a clean slide and air dry. Other swabs: swab the affected site and break the swab into UTM or enat medium * Urine: send 10-20ml of urine in a sterile container with no preservatives. * UTM or enat medium is available from the RVL.

6 TABLE 1 - TESTS AVAILABLE Agent Assay method Sample required Typical turn around time for non-urgent requests (days)* Adenovirus (respiratory) PCR Respiratory samples, eye swab, urine, EDTA blood 5 PCR Faeces 5 Adenovirus (faecal group F) Arboviruses Serology (SAT) Clotted blood 21 Astroviruses PCR Faeces 5 Bocavirus PCR Respiratory secretions 5 Bordetella pertussis PCR Respiratory secretions 5 Chlamydia trachomatis Respiratory Coronaviruses PCR Urine or genital swab 5 PCR Respiratory samples 5 Cytomegalovirus (CMV) Enteroviruses (picornaviruses) Serology IgM Clotted blood 8 Serology IgG Clotted blood 3 PCR qualitative / quantitative EDTA blood, urine & other specimens 5 PCR Faeces, clotted blood, 5 CSF & throat swabs (inc Coxsackie & ECHO viruses) Epstein Barr virus Serology Clotted blood 8 (EBV) PCR qualitative / EDTA blood 5 quantitative Erythrovirus B19 Serology IgM Clotted blood 8 (parvovirus B19) Serology IgG Clotted blood 8 PCR Clotted blood 5 Hantavirus (SAT) Serology Clotted blood 21 Hepatitis A virus Serology IgM Clotted blood 3 Serology IgG Clotted blood 3 Hepatitis B virus Screening for Clotted blood 3 infection (HBsAg) Markers Clotted blood 3 Anti-HBsAg Clotted blood 3 Molecular Clotted blood 5 quantitative Pre-core mutant Clotted blood 30 analysis (SAT) Lamivudine Clotted blood 30 resistance analysis (SAT)

7 Hepatitis C virus Serology Clotted blood 3 PCR qualitative / Clotted blood 8 quantitative / Antigen Genotyping Clotted blood 21 Hepatitis D virus Serology (SAT) Clotted blood 21 Hepatitis E virus Serology (SAT) Clotted blood 21 Herpes simplex virus Serology IgM Clotted blood 8 (HSV 1 / HSV 2) PCR CSF, genital, skin & 5 eye swabs Human herpes virus 6 Serology (SAT) Clotted blood 21 (HHV6) Human Serology Clotted blood 3 immunodeficiency Molecular EDTA blood 14 virus quantitative (viral load) (HIV) Congenital EDTA blood 21 transmission (SAT) Genotypic EDTA blood 30 resistance testing Human T- Serology Clotted blood 10 lymphotropic virus (HTLV) Influenza viruses PCR Respiratory samples 5 Legionella PCR Respiratory samples 5 pneumophila Measles virus PCR Respiratory samples 5 Serology IgG Clotted blood 5 Serology IgM (SAT) PHA, through a CCDC, provide a saliva collection kit Human PCR Respiratory samples 5 metapneumovirus (hmpv) Molluscum EM Skin material 10 contagiosum Mumps virus PCR Saliva / Urine 5 Serology IgG (SAT) Clotted blood 21 Serology IgM (SAT) PHA, through a CCDC, provide a saliva collection kit Mycoplasma PCR Respiratory Secretions 5 pneumoniae Norovirus PCR Faeces, vomit 5 Orf virus EM Skin material 10 Parainfluenza viruses PCR Respiratory samples 5 Pneumocystis jiroveci PCR Respiratory samples 5 (carinii) Polyomavirus BK PCR EDTA blood, urine 5 Polyomavirus JC PCR (SAT) CSF 21 Q fever (Coxiella burnetii) Serology IgM, Phase I & II Clotted blood 10 immunofluorescence Contact the PHA Tel: Contact the PHA Tel:

8 Rabies virus Serology IgG Clotted blood 30 (SAT) Respiratory syncytial PCR Respiratory samples 5 virus (RSV) Rhinovirus PCR Respiratory samples 5 Rotavirus PCR Faeces 5 Rubella virus Serology IgM Clotted blood 8 Serology IgG Clotted blood 3 Varicella zoster virus Serology IgM Clotted blood 8 (VZV) Serology IgG Clotted blood 5 PCR CSF, genital & skin swabs 5 * N.B. urgent requests will, by arrangement, be completed in a faster timeframe appropriate to the clinical indication. KEY CCDC Consultant in Communicable Disease Control CSF Cerebrospinal fluid EM Electron microscopy PCR Polymerase chain reaction PHA Public Health Agency Tel: SAT Send away test

9 TABLE 2 - CLINICAL INDICATIONS FOR TESTING Provisional Diagnosis/ Clinical Situation/Symptoms Agents Specimens Respiratory infection (URTI & LRTI) Pneumonitis immunocompromised patients Influenza A & B, RSV, rhinovirus, adenovirus, parainfluenza 1, 2 & 3, coronavirus, metapneumovirus, bocavirus Q-fever, Chlamydia group, Mycoplasma pneumoniae Pneumocystis jiroveci(carinii) Respiratory specimen Respiratory specimen Respiratory specimen Hepatitis Hepatitis A, B & C, Epstein Barr virus, CMV Clotted blood Gastrointestinal Rotavirus, adenovirus, norovirus, astrovirus Faeces, vomit Central nervous system (meningitis & encephalitis) Herpes simplex, varicella zoster, measles, mumps, enteroviruses, HTLV-1, JC virus Faeces, CSF, throat swab in UTM or enat medium *, clotted blood Arthralgia Erythrovirus B19 Clotted blood Skin rashes Rubella, measles, erythrovirus B19, herpes simplex, varicella zoster, molluscum contagiosum Conjunctivitis Adenovirus, herpes simplex, enterovirus Eye swab Stomatitis Lymphadenopathy & glandular fever Herpes simplex Epstein Barr virus, CMV Clotted blood and vesical or skin material if appropriate Swab in UTM or enat medium * clotted blood Clotted blood Pleurodynia Enterovirus Faeces, clotted blood Hand, foot & mouth disease Enterovirus Faeces, vesicle fluid Myocarditis Enterovirus Faeces, clotted blood Endocarditis Q fever Clotted blood Immunity testing (postvaccine) Immunity testing (natural exposure) Genital infection AIDS & HIV Embryopathy Hepatitis B, rubella, measles (SAT) CMV, EBV, erythrovirus B19, hepatitis A, varicella zoster, measles (SAT) Herpes simplex, T pallidum Chlamydia trachomatis HIV Loads, Mutational Analysis, Genotyping Erythrovirus B19, CMV, rubella Clotted blood Clotted blood Swab in UTM or enat medium * First catch urine, swab in Abbott collection kit Clotted blood EDTA Blood Clotted blood & fetal tissue Head & neck tumours Epstein Barr virus Clotted blood

10 Renal / dialysis Hepatitis B & C, HIV, CMV Clotted blood Organ donors Hepatitis B & C, HIV, HTLV, CMV, Syphilis Clotted blood * UTM or enat medium (available from RVL) The above table indicates the most likely infecting agents, but is not intended to be an exhaustive list. Other investigations will be carried out by arrangement